We Need you Alive
by geradsredskittle666
Summary: Atlantis never gives McKay a break and McKay becomes sick. But someone hurts him worse and its up to his friends to help him recover. Warnings for slash, rape, and homophobic language. Slash. McKay/Sheppard pairing.
1. Chapter 1

We need you alive

AN: So just recently gotten obsessed with this show, excuse any errors and show related misspellings. If you are aware of my work on Mea Culpa, you know to expect a high level of whump. Here goes my first published Stargate Atlantis work!

Disclaimer: I don't own Stargate Atlantis and any of its plots or characters. I write for entertainment and do not make profit off this work.

Warnings: slash (thats male/male pairings), abuse centric.

Pairings: Sheppard/McKay

START

It had been 36 hours since he had slept. Rodney McKay, Atlantis's resident genius and one of the few who knew the city so well was working on more repairs. The city was old. It was only natural that so much would need fixing or would just break. At first he had hated it. What use was a broken city? Still the city had grown on him. He felt like a father as his city showed more and more to him as he fixed her. When she had flourished and even flown, he felt immense pride. The city knew who would fix her and he would do anything for his city.

It had been a quick repair. The city had offered little resistance. So he made his way to his quarters to try catch some sleep before the next call. It was inevitable. His city and his friends needed him.

He winced as another headache showed itself. He pushed back the pain and continued. A sudden wave of dizziness hit and he balance himself against the wall.

"Dr McKay, are you okay?" he heard a marine ask.

"What?" he asked through the haze of pain. The tone lacked his usual sharp edge. Though he quickly recovered. He put on a neutral expression "Yes, just missed lunch. Just heading there after I get something from my room" he excused.

The marine paused but smiled back. "If your sure. We need you at your best. We may not say it but we are thankful you have saved us many times. Most of us just don't understand a lot of what you do." he said respectfully.

Rodney actually smiled back "Thanks." The military types often acted like he didn't belong here. They thought that since he didn't carry a gun and shoot bad guys, he wasn't useful. Of course he did shoot bad guys sometimes but not like the non science men of the base.

The dizziness had faded so he could now walk to his room. He found some migraine pills in his room and took them. He found some cold pills too. He could feel himself getting sick for a while. Just a cold. Nothing that would trump the time needed for his friends and city.

Of course he knew he was not in top condition. He barely slept on a normal schedule. Some days or weeks he was busy all the time. He ate when his team ate. It was almost like they were making sure he had time for food. Since they had learned of his conditions, they had taken to helping him. One would often find him when it was meal times and they would eat together. He didn't think it was all Shepards idea either. He would encourage it though. Everyone had been busy the past 3 days anyway. Rodney had simply forgotten, finding power bars when he felt dizzy. He wanted a hot meal but he was so tired. Sleep would have to come first.

He was almost asleep when he heard the radio spark to life. Instinct made him reach out for it. "Sheppard to McKay" he heard.

He pushed himself up, his vision blurred and he coughed loudly. The echoing sound didn't sound great. The migraine pain increased when he moved his chest forward with the coughs. _Get a grip McKay!_

"Rodney?" he heard over his radio again. John sounded worried.

"Sheppard." Rodney replied, willing his voice to stay strong.

"You had me worried. We have a problem with a generator" John reported.

"Can't Zelenka handle that?" Rodney complained.

"He said you might wanna take a look. He says its in section 3." John just replied, unfazed by his friends sharp tone.

"On my way" Rodney replied before gathering his equipment.

Rodney felt sick. Really sick. He might have freaked out but he had a job. Sheppard had asked him to.

He pulled himself to the edge of the bed. He was dizzy again and his stomach felt uneasy. He tried to focus on something else. A distraction from his current problems. His mind felt fuzzy but he got his breath back and could focus. He took the least populated route and started work on the power problem.

He didn't know how long later but he distantly heard his radio. He tried to reach for it but he felt heavy. Pain interrupted his thoughts and his mind was fuzzy. It was difficult to breath but he didn't seem to care. The one part of him that was panicking found his voice. "Shep...ed" he slurred in an attempt to contact the man. He knew he had to try. It had to be enough. He felt darkness claim him.

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Sheppard tried to calm down. It had been hours since Rodney had said he would fix the generator. His friend hadn't checked in yet. Maybe he had got so lost in his work he had forgotten. John had a bad feeling...

"McKay!" he called in his tone he often used in the field to keep his friend focussed.

"McKay!"

"Rodney!"

He swore softly. Turning to Elizabeth he said "I'm going to find him. Tell Carson to have a team ready" he ordered before leaving.

He found Rodney where he was fixing the generator.

He leaned down to check his fallen friend. Rodney looked sick. He was pale and seemed in pain. John could feel a fever too. He could barely breath and to his horror, John found splatters of blood on his friends palm. More blood wiped on his uniform. He wasn't responding to John's attempt to wake him.

How long had he been so sick?

Recovering slightly he spoke into his com "Carson come quick. His sick.".

Carson had attempted to ask for more information but Shepard tuned him out. He took Rodney's hand and muttered comforts. He ran a hand through his friends sweat soaked hair. The action seemed to sooth his friend.

It wasn't until he felt Carson's hand on his shoulder that he noticed the other man. "Come on lad" Carson said gently.

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Shepard woke again in the infirmary. Carson noticed and went over immeaditly.

"Feeling better?" he asked.

John nodded. "Hows Rodney?" he asked urgently.

Carson paused. "He will be okay. You found him in time. He had a cold but he didn't treat it so it became pneumonia. His blood sugar was dangerously low. I don't think his been eating much this last few days. He told me before he hadn't slept for 36 hours either. I told him to get some sleep after his current task. He seems to be responding to medication." he explained.

"He looked so sick." John said. Since Rodney saw Carson for even the smallest of things, none of his team had seen him sick. Shot maybe but that was usually fixed.

"Aye and he was. He should have come straight to me!" Carson replied sharply.

"I asked him to fix the power. I didn't think..."John trailed off.

Carson softened at the guilt. "It not your fault. He works hard for us. Sometimes people forget his human. A genius but a human." he said softly.

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John was cleared for duty. As soon as he could he was at Rodney's bedside. The scientist was asleep but he was looking better. He was less pale for one. Thanks to the medication he could breath properly and was in less pain. The blood had been cleaned off him. His fever had significantly dropped. John was glad for that. The stubborn man would make it.

Still Shepard felt guilty. If he hadn't asked Rodney to work, the scientist would be sleeping. Of course he was going to get sick anyway. At least this way someone had been around to help him.

He took the sleeping mans hand in his own. "Rodney buddy, you need to get better. You scared me. I don't know what I'd do" he said quietly. He was alone so no one could hear him but he still felt nervous. He cared for Rodney more than a friend should. If the military found out he could get in trouble. Besides Rodney had been dating women on Atlantis.

John started to feel tired himself but refused to move. When McKay woke, it would be to his face. Soon he was asleep, his head resting on the blankets before him. Unknown to him Carson had seen them. The doctor smiled at the pair. He remembered when Rodney had confessed to him.

 _Flashback:_

 _Rodney was figiting more than usual. Even the smallest task was next to impossible for Carson. "Now now, whats on your mind?" he asked gently. He hoped Rodney would be suitably distracted._

 _The scientist had looked up surprised. "I don't know if I can tell." he had said hesitantly._

 _Carson frowned._

 _Finally McKay spoke. "I think I love him. I want something but I know its out of reach. I'd ruin his career. Not that he is gay. Or that anyone could like me..."he said in a depressed tone._

 _Carson had caught on. Without stopping bandaging, he just smiled back. "Thats not true! I'm sure someone likes you. For what its worth, I don't think Sheppard would care either. Even if he is straight." he had said casually._

 _End flashback_

Carson was sure that John loved him back. He saw the concern when his friend got hurt. He saw the looks across the room when he thought no one was looking. He saw the smile that was saved just for his friend. The truly relaxed smile that said he trusted Rodney above all.

He grabbed a blanket and out it over Shepard before leaving them. It was sweet.

The gesture didn't wake the pair. John shifted in his sleep but otherwise didn't react. Rodney must have felt it because he smiled contently.

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Rodney work that next morning feeling better than before. He could breath much easier! His migraine was a now a dull ache. The fuzziness had also faded. He still felt sick but not nearly as much as before.

He looked down and froze. What was John doing there? Why hadn't he returned to his room? John remained asleep on Rodney's leg still holding tight to his hand.

"He was terribly worried." Carson said.

Rodney just looked away.

"He wouldn't leave you." Carson spoke again.

Rodney still hadn't even looked at him.

"Whats on your mind?" asked Carson softly. It was unusual behaviour.

It seemed at first that Rodney would refuse to speak but to Carson's relief he spoke. "Don't give me false hope. I know that he can never feel that way. I don't wanna even think that this means anything other than friendship." his spoke, his voice cracking as he spoke angrily.

The doctor just sighed. He was worried that this would hurt McKay more. McKay was prone to depression and anxiety as well as many others. He would speak to McKay's team. Just to be sure.

"Fine. How are you feeling?" Carson said professionally.

Rodney brightened up. "Much better. Migraine is almost gone and I can breath again. Still abit fuzzy and nauseous." he said softly.

Carson was relieved to hear that. He had been worried when he first saw Rodney on the floor but he was responding well to treatment. "That would be the fever. Its much lower now. Hopefully by tomorrow the fever will break. Let me know if you feel like throwing up or if the pain returns. When you get better though, I need to speak to you."

Rodney looked pleased. "So I'll be out soon?" he pleaded.

Carson had to laugh. "If all goes well a week at most."

At this point Sheppard woke. He froze when he realised his position. Even more confusing was the fact his friend had not moved his hand even though he could hear him speaking. Carson left, hoping the boys would sort out their feelings sooner rather than later.

Rodney smiled at his friends bed hair and confusion. It was almost cute. No it was cute.

"McKay you alright?" he heard in a worried tone.

He then realised that he had been staring like a school girl. "Just thinking" he excused.

Clearly John had seen the lie but didn't press him. Still that content smile was cute he thought. He hoped he could be the one to put it there but knew better. Rodney dated girls and always made a point to comment on girls. Even voicing a desire to be kidnapped by a hot alien girl once.

"You look better. Feel better?" he asked hoping the guilt didn't show.

"Yeah much. Carson says I might be out in a week if I keep improving." he replied easily. He had heard the extreme worry. More than just a team member or friend. Guilt too. That concerned him. Guilt over what? Rodney had done this too himself.

Teyla and Ronon choose to join them at that point. "Elizabeth wanted to see you. She was worried when you were not in your room this morning but I told her you might be here." Teyla spoke.

Ronon grinned. He saw that John and Rodney loved each other. It wasn't that hard to spot. Not that they would admit that. "Clearly you slept here then." he added.

Shepard just nodded. "I'll see her in a bit."

"I see you are keeping Rodney company. I'm sure she will wait." Teyla spoke. She saw the way John firmly held Rodney's hand. She read his protective posture. It was clear to all of Atlantis that they were in love. They were perfect for each other. Rodney didn't even attempt to break the hold on his hand. Both still looked regretful.

Rodney allowed himself to be happy in that moment. He was with his team. John was making him feel safe. It was perfect. Life didn't throw many perfect moments his way so he allowed himself to relax.

Before John realised his feelings toward him and sent him back to earth.

AN: As usual read and review.


	2. Chapter 2

We need you alive

AN: So just recently gotten obsessed with this show, excuse any errors and show related misspellings. If you are aware of my work on Mea Culpa, you know to expect a high level of whump.

Disclaimer: I don't own Stargate Atlantis and any of its plots or characters. I write for entertainment and do not make profit off this work.

Warnings: slash (thats male/male pairings), rape centric, non graphic rape, homophobic language and actions.

Pairings: Sheppard/McKay

START

Rodney had been discharged with some medication just in case and a warning to return if he even felt a slight cold coming on. Rodney remembered the conversation that Carson had with him in private.

 _Flashback:_

 _Carson had taken Rodney to his private office. For Rodney's reassurance more than his own he instructed his nurses to not bother him unless it was an emergency. Still he had checked and ensured each patient under his care was okay before. The nurses had little work to do._

" _Now son, you know what I want discuss?" he had started kindly._

 _Rodney had an idea. He simply nodded._

 _Satisfied the doctor continued. "How long were you sick before I found you?" he asked._

" _I had a cold. I didn't think anything of it. Two days before I arrived I felt sick. I knew I had to see you but I had things to do. It was only that afternoon that I started getting really sick. I was going to see you after I repaired the power." Rodney explained._

" _Aye lass but surely you knew that not taking care of yourself would make it worse for you? You are a genius right? Thats what you keep saying. Smartest man in two galaxies?" Carson scolded gently._

 _Rodney rolled his eyes. "I forget okay? Usually John or Teyla or Ronon find me. No idea how but I just get caught up." he said only slightly annoyed. How could he be annoyed when Carson only cared?_

 _Carson approved of that. He would ask the team to keep that up and keep an eye on Rodney._

" _Well that and sleep." he reminded sharply._

" _I sleep when I can. You know I have a city that needs me. Or its people that need saving." Rodney quickly excused._

 _Carson knew that Rodney was right. Atlantis and Elizabeth ran him ragged. Then they let him run the science department. Then they let him join an off world team. It was too much. No matter how smart or needed a man was. "Yeah" he echoed quietly. "You should ask for time off. You do enough. I could ask Elizabeth for you, for medical reasons of course."_

 _Rodney smiled at that. "You know as well as I do that even if she did I would still be called at all hours of the night and day."_

 _Carson only gave him a small smile. "Yeah I do. I still don't think its fair."_

 _Rodney laughed and said bitterly "life's not fair"._

" _I'll speak to her anyway. Maybe we can at least limit your night time calls" the doctor said calmly._

" _I'll try okay? I can't promise I won't forget meals or that I will actually get a full nights sleep." Rodney had said softly._

" _Thats all I ask. Call me if you feel sick too." added Carson._

 _End Flashback._

Rodney had gone to his room to try sleep. It was another week of taking it easy before he could work. Well be seen working anyway.

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Carson had called all of Rodney's team mates to his private office. Though he had released Rodney he knew his chances of returning were high. He needed to take care of himself.

"I'm sure you share my concerns" he started, looking at the gathered team members. The all mirrored his own concerned face. "McKay through no fault of his own, needs our help."

Teyla was the first to speak "Of course. You know we will. We are his friends." she said in her calm voice.

Carson smiled at that. "He needs us to help him take care of himself. I would ask you to help him ensure he eats all his meals. Don't let him forget or say no."

When he received accepting nods from everyone he continued. "My other concern is his sleeping patterns. His skills mean that he can be called any time. Even when he is having some much needed rest. His duties are overwhelming for one person."

Again everyone accepted that.

"We know doc. We will do our best for him." Sheppard had stated without even hesitating. His team knew what to do. Rodney was part of their family. Part of Atlantis's family. Even if he didn't know it.

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The team were staying overnight at with Teyla's people. As usual Rodney and John shared a tent. Teyla had made sure Rodney ate at the feast. She had ensured that anything near him was citrus (and anything else on the growing list of allergies) free.

John wasn't tired. He lay on his back watching Rodney try sleep. Eventually Rodney fell asleep. John was happy with that. He was about to drift off himself when he heard whimpers.

Rodney was tossing and turning. He held his arms up to protect his face. He whimpered and spoke out loud. "Please" he pleaded. "I'm sorry" he said pitifully. "Stop" he pleaded. "I didn't mean to do this" he pleaded louder.

John worriedly tried to wake him. After a few minutes Rodney woke panting and sweating. He spotted John and his concern and blushed.

"Sorry If I woke you." he said regretfully.

John frowned. "You didn't. Even if you did, I could never be even the slightest bit annoyed. Your my friend. If you need me, I'm here." he said firmly.

Rodney could only nod.

"Want to tell me what your nightmare was?" John asked concerned.

Rodney hesitantly looked away. "Just my uh crush...yes lets say crush rejecting me." he said in as little detail as possible. "I ruined things. He...uh they" he quickly corrected "were angry at me."

Shepard frowned. "Thats not fair to you. Maybe this crush of yours isn't so nice then" he said protectively.

Rodney smiled wistfully. "Nah she...uh they I mean would not hurt me. I can never tell him...uh them though. It would ruin everything." he said nervously.

John closed the distance between them in a hug. He spoke firmly in his friends ear "You know if you think I care who you date be it man or woman, your an idiot. As long as they make you happy and treat you right, there okay by me". He could still feel McKay's shaking and his rapid heartbeat. Rodney had quietened down now. He slowly became less tense and settled his head on Shepard's shoulder. John could feel the deep even breaths on his neck. It gave him butterflies just thinking about it.

Rodney was asleep. He was also smiling contently.

John smiled himself at that. It made him glad that he could make his friend so happy. Carefully he settled Rodney back down. The man didn't even stir. He whined softly at the loss of contact but remained asleep.

Satisfied Shepard fell asleep himself.

The next morning McKay seemed happier than he had in a long time. John approved.

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His happiness would be short-lived. News of Sheppard's behaviour had spread. It was said in rumours that John and Rodney were dating and didn't want anyone to know.

No one asked John of course. The respected team member had the rank to make their lives hell. No one crossed an angry Sheppard unless they were suicidal!

The same couldn't be said of his supposed boyfriend.

Rodney had finished in the labs and was just leaving for the night.

He made his way to his rooms. He noticed some marines following behind him. They didn't look familiar. Must have come from Earth in the new batch of newbies. He felt uncomfortable but decided it was just coincidence.

START RAPE AND HOMOPHOBIC SCENE (Don't read if it triggers you).

Until they slowed down as he did. He saw terrifying smirks as they eyed him. "Don't bother running. We got you where we want you fag!" they called out loudly.

Rodney froze. Had Carson betrayed his secret? Had John and he been observed? No, it was probably speculation. Still these men looked dangerous. He was no match for them and there was no where to run.

The leader nodded to his friends. They took his arms and roughly held him back. He tried to squirm free but they held tighter. He tried to kick them but they were purposely out of range.

He tried to calm him racing heart. He tried to even out his panicked breaths. He had to relax if he was going to get free. Make a plan.

"Oh you won't be going anywhere soon. When I'm done your precious Sheppard won't even want to look at you." the leader taunted calmly.

Rodney struggled again. He tried not to acknowledge what the leader meant.

The leader smirked at him. He looked happy now. Rodney tried to prepare himself for what beating lay ahead. He gasp as he felt punch and kick after punch and kick anywhere the limbs could reach him. Holding back the pain was a fruitless task. His body hurt. New bruises were hit only making the pain worse.

Soon Rodney could no longer support himself. He was held up by the marines only. He whimpered. He felt a sharp slap. "I heard you were a filthy cock sucker. Lets see how good you are." the leader spoke with venom.

Rodney froze. The marine could not mean what he thought. He felt cold. He felt wetness on his face.

The marine growled. "Listen up faggot, you open up or I'll do it for you." he angrily spoke.

When Rodney didn't move he glared. In one swift movement he smashed Rodney's head against the wall. The pain surprised Rodney. He gasp loudly in pain. In one swift movement the assaulting marines penis was in his mouth and moving.

Rodney tried to move away. He desperately struggled. He found fight in his broken body. It did no good. He whimpered and let himself cry.

After 10 minutes the marines heard a noise. The marine pulled out and the three gathered their guns. They left Rodney in a whimpering pile as he curled up in defence of any more attack. He shut out the world and the pain.

END RAPE AND HOMOPHOBIC SCENE.

"Only chance you get. Come out." Shepard called.

The marines froze. He would be more than mad. The leader was still cocky though. "Come to collect your fag? You won't want him anymore. Not after what I have done!" he said happily.

Shepard glared at him. It was a dark glare that promised revenge. He glanced at his friends curled up sobbing form. His grip on his gun tightened.

"Oh he was good too" the marine said gleefully.

In seconds he was on the floor with two new bullet wounds. Non fatal of course.

A team secured the uninjured pair and the now injured leader. John paid them no mind as he headed straight for Rodney.

Ronin and Teyla had their guns aimed at the guilty men. It was only remarkable self restraint that no one had shot them yet. The men knew that and the uninjured pair were looking frightened.

Rodney was much too pale and seemed in bad pain. That wasn't what worried him most. In fact because his friend was curled up, he could not see the injury. He saw the blood on the wall though. Impact. A head wound.

Rodney was distressed. He had to calm him down so Carson could treat him. John sat and started playing with Rodney's hair. "Its okay now. I'm here. Your safe." he said softly. He hoped he could get through to the distant man.

After a minute he heard his friends voice. "Safe?" Rodney asked in broken voice.

"Always" he affirmed back.

John could feel his friend shaking and tensed. He managed to pull the man into his lap. The pair silently sat as Rodney was comforted. Soon the man relaxed and uncoiled from his ball. No one said anything or acted like it was different. It was no place for that.

Carson entered the scene and ordered some of his team to the injured marine. He approached Rodney with a few of his own team. The first thing he noticed were the pairs position. John looked protective. His glare scaring some of the marines even. Rodney looked tense but calmer with John so close by.

He smiled at the pair. "I'm going to lift your shirt up to see your injury. Okay?" he asked softly. He had heard some of what had happened from Teyla. It disturbed him greatly. He knew that he would need to be more careful than usual.

Rodney whimpered and look to John. John ran his fingers through his friends hair again. "Your safe okay. You know Carson would never hurt you." he said calmly. Rodney paused then nodded.

Carson looked worried now. The reaction only confirmed what Teyla has told him might have happened. Rodney had never been frightened of him before. Rodney was even less trouble for him than any of his staff. "Just tell me if you want me to stop okay?" he said to reassure his patient. He noted the nervous glance in John's direction and the shaking. He pulled up the shirt to see bruises covering Rodney. It was a sickening mix of blue, black and purple. "I'll need to get some scans. I can't tell of anything is broken or bleeding from here."he muttered.

"His head too, Doc" John said quietly.

Carson inspected that too with worry. "We need to get you back Rodney." he said calmly. Rodney seemed to tense at that.

John noticed quickly that his friend was panicking and calmed him down. "Your safe. I'll make sure he doesn't get you." he said firmly. John turned to Carson now. "He will need a private room. That marine that was shot hurt him. He was making him do sexual things..."John said carefully before looking away. For his own discomfort at the idea or Rodney's panic, Carson was unsure. Maybe even both.

Carson paled. He pushed back the sick feeling and focussed on being cold and detached. "Of course. I trust you will post guards?" he asked.

John nodded.

Rodney still didn't want to move. He seemed to cling to John. Carson smiled. "Sheppard can visit as soon as I have taken a better look at you. Its hard to tell if your more injured than I can see. I don't want to see you hurt. You know I'll make sure your safe." he said kindly.

Rodney looked at John who nodded in confirmation.

Finally Rodney let Carson take him to the infirmary. Carson barked orders into his head piece to prep for the arrival and scans. John barked orders for the security teams for McKay to be arranged.

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Teyla and Ronin caught up to Sheppard who was quickly securing all the loose ends now. They could see he was in no shape to be working, even behind his military mask of no emotions. "We can do this" Teyla said quietly. Ronin grunted.

John hesitated but he trusted his team. He knew Teyla could handle any unruly men and any diplomatic duties. Ronin could more than handle any problems. Any marine who even thought to defy the pair would be put in their place. He nodded his acceptance not trusting his voice.

Barely paying attention to the other marines, he went to his room. His mask was slipping and McKay needed him to be strong.

AN: Read and review as always.


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